Contacts of the strand formed by residues 40 - 46 (chain E) in PDB entry 1PPE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 40 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E SER* 2.7 28.4 + - - +
33E LEU 3.7 4.9 - - - -
34E ASN* 3.5 7.4 - - - +
39E TYR* 1.3 84.5 - - - +
41E PHE* 1.3 61.6 + - - +
42E CYS 3.1 30.2 + - - -
43E GLY* 4.0 1.8 - - - -
73E ILE* 4.4 20.6 - - + -
141E TRP* 3.8 45.0 - + + +
193E GLY* 2.9 26.0 + - - -
7I LEU* 3.5 20.4 - - + +
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Residues in contact with PHE 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.1 40.4 + - + -
34E ASN 3.8 2.7 - - - -
37E SER* 3.4 35.9 - - - -
39E TYR* 3.8 10.3 - - + -
40E HIS* 1.3 80.8 - - - +
42E CYS* 1.3 83.7 + - + +
58E CYS* 3.2 29.8 - - + -
60E LYS* 3.6 28.5 - - + -
63E ILE* 4.0 11.4 - - + -
193E GLY* 3.8 3.6 - - - -
6I ILE* 3.8 8.4 - - + -
7I LEU* 3.0 47.7 + - - +
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Residues in contact with CYS 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 2.9 30.3 + - + -
40E HIS* 3.1 16.0 - - - -
41E PHE* 1.3 99.0 - - + +
43E GLY* 1.4 65.8 - - - +
58E CYS* 2.0 53.6 - - + -
193E GLY 4.3 3.6 - - - -
195E SER* 3.2 16.2 - - - +
6I ILE* 3.8 10.1 - - - -
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Residues in contact with GLY 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLN* 4.1 9.0 - - - -
31E VAL 3.4 13.0 - - - -
33E LEU* 3.7 8.7 - - - +
40E HIS* 4.0 5.6 - - - -
42E CYS* 1.4 75.7 - - - +
44E GLY* 1.3 52.2 + - - -
54E SER* 2.7 28.9 + - - -
140E GLY* 6.4 0.7 - - - -
193E GLY 4.2 4.2 + - - -
194E ASP* 4.2 2.1 + - - +
195E SER 2.6 13.8 + - - +
196E GLY 3.5 6.9 - - - +
197E GLY* 4.1 4.9 - - - -
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Residues in contact with GLY 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E TYR 3.8 1.0 - - - +
30E GLN* 3.8 4.2 - - - -
31E VAL* 3.2 37.3 + - - +
43E GLY* 1.3 73.5 - - - -
45E SER* 1.3 63.2 + - - -
52E VAL* 4.3 2.7 - - - -
53E VAL 3.2 13.9 - - - -
54E SER* 4.2 2.7 - - - -
196E GLY 3.2 9.3 + - - -
197E GLY* 3.9 2.0 - - - -
198E PRO* 3.9 7.4 - - - +
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Residues in contact with SER 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E TYR* 3.3 8.7 - - - -
44E GLY* 1.3 74.7 - - - -
46E LEU* 1.3 62.1 + - - +
47E ILE* 3.5 0.7 + - - -
52E VAL* 3.1 6.2 - - - +
53E VAL* 2.8 47.2 + - - +
121E ILE* 3.8 21.5 - - - -
196E GLY 4.9 0.7 + - - -
197E GLY 4.5 0.7 - - - -
198E PRO* 3.4 29.1 - - - +
209E LEU* 3.6 9.2 - - - +
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E PRO 5.0 1.1 - - - +
29E TYR* 2.9 16.4 + - - +
31E VAL* 4.1 9.7 - - + +
45E SER* 1.3 68.4 - - - +
47E ILE* 1.3 59.9 + - - +
48E ASN 2.9 24.2 - - - +
49E SER 4.5 2.2 - - - -
51E TRP 3.7 7.9 - - - +
52E VAL* 4.0 16.2 - - + +
67E LEU* 3.9 12.3 - - + -
108E LEU* 4.1 16.2 - - + -
112E ALA* 4.8 0.9 - - + -
114E LEU* 3.9 19.1 - - + -
118E VAL* 3.8 29.2 - - + -
119E ALA 3.8 18.2 - - - +
120E SER* 3.2 2.4 - - - +
121E ILE* 3.0 28.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il